Chapter 7.2

Question 1

What is the purpose of the 5’ Cap?

Answer 1

The 5’ cap is a methylated GTP molecule that is added during transcription. This molecule protects the mRNA from degredation in the cytoplasm. It is also recognized by the ribosome as a binding site.

Question 2

What is meant by alternative splicing?

Answer 2

Depending on how a single transcript of hRNA is spliced, you can get different proteins. This is hypothesized to make it so we can fit more potential proteins into a smaller amount of DNA/RNA. For example, the same segment of DNA and the hnRNA transcript that goes with it could be spliced 5 different ways to make 5 completely different proteins.

Question 3

What is the purpose of the 3’ Poly- A tail?

Answer 3

The 3’ Poly A Tail is a long chain of Adenines. The Poly A tail is a shield for the mRNA transcript in the cytoplasm. As soon as the mRNA transcript hits the cytoplasm, the poly A tail starts to get destroyed. The longer the Poly A tail, the more time the mRNA transcript has to get translated. Also asists with export from the nucleus

Question 4

What is a UTR?

Answer 4

UTR stands for untranslated region. It refers to small portions at the ends of the RNA transcript that do not get translated. Remember, Translation always starts at AUG and ends at stop codons, so UTR’s are just the mRNA before the start codon and after the stop codon.

Question 5

What is the ribosome?

Answer 5

The ribosome is a structure made of proteins and RNA that associates with mRNA in the cytoplasm and constructs chains of amino acids using tRNA’s.

Question 6

What are the three binding sites for tRNA’s in ribosomes?

Answer 6

1. A - AminoAcyl Site
2. P - Peptidyl Site
3. E - Exit Site

Question 7

What are the three main steps of translation?

Answer 7

1. Initiation
2. Elongation
3. Termination

Question 8

What are the necessary requirements for each step of translation?

Answer 8

1. Initiation - Initiation Factors and GTP
2. Elongation- Elongation Factors and GTP
3. Termination - Releases Factors and GTP

Question 9

What is the Shine-Dalgarno sequence?

Answer 9

The Shine-Dalgarno sequence is seen in prokaryotes. It is a piece of RNA in the 5’ UTR that allows the small sub unit of the ribosome to bind.

Question 10

If prokaryotes use the Shine-Dalgarno sequence to recruit the small sub unit of the ribosome, how do eukaryotes do it?

Answer 10

Eukaryotes use the 5’ cap to recruit the small sub unit of the ribosome.

Question 11

Describe Initiation of translation

Answer 11

First, the small ribosomal sub unit binds to the mRNA (using shine-dalgarno in prokaryotes or the 5-cap in eukaryotes) and scans for start codon.

Second, the activated initiator tRNA (fMet in prokaryotes and Met in eukaryotes) binds to the start codon through base pairing at the P site of the small ribosome.

Third, the large sub unit binds to the small sub unit with the help of initiation factors, forming the completed initiation complex.

Question 12

Describe the role of the A site

Answer 12

The A site holds the incoming aminoacyl-tRNA. This is the next amino acid that is being added to the growing chain.

Question 13

Describe the role of the P site?

Answer 13

The P site holds the tRNA that carries the growing polypeptide chain. It is also where methionine (starting AA) binds during initiation. In this part of the ribosome, an enzyme called peptidyl transferase uses GTP to transfer the peptide chain from the tRNA in the P site to the tRNA A site.

Question 14

Describe the role of the E site.

Answer 14

After a tRNA in the P site loses its peptide chain, it is transferred to the E site where it pauses for just a second before dissociating back into solution so it can be recharged.

Question 15

What are Elongation Factors?

Answer 15

Elongation Factors are proteins that speed up elongation by bringing in tRNAs and GTP. Elongation Factors also get rid of GDP (used up GTP) so that fresh GTP’s can take their place.

Question 16

What is a signal sequence?

Answer 16

A signal sequence is a part of the new peptide chain that directs the ribosome to move to the rough ER and finish translation there. Signal sequences are meant for proteins that won’t be in the cytoplasm, which includes secretory proteins (like hormones and digestive enzymes), membrane proteins, and lysosome proteins.

Question 17

Describe Elongation in translation.

Answer 17

First, the appropriate tRNA will enter the A-site of the complete ribosome.

Second, GTP is used to transfer the polypeptide from the tRNA in the P site to the tRNA in the A site.

Third, GTP is used to move the tRNA from the P site into the E site, and the tRNA in the A site to the P site. This also moves the ribosome one codon down the mRNA.

Elongation factors are responsible for moving it down a a codon

Fourth/First, the tRNA leaves the E site and the next appropriate tRNA binds the A site.

Question 18

Describe Termination of translation?

Answer 18

When a stop codon moves into the A site, a protein called Release Factor binds to the codon and causes a water to be added to the chain. Next, termination factors and peptidyl transferase hydrolyze the peptide chain from tRNA. The ribosome will dissociate shortly after.

Question 19

What is post-translational processing and what are the commom types?

Answer 19

Post-Translational processing refers to any modifications made to a protein after it has already been translated.

A. Folding by chaperones
-bonus: signal pepties
B. Cleavage events (signal sequence needs to be cleaved for function)
C. Adding biomolecules
1. Phosphorylation
2. Carboxylation
3. Glycosylation
4. Prenylation

Question 20

Generally speaking, how does phosphorylation affect proteins?

Answer 20

Addition of phosphate groups. Phosphorylation is used to activate or deactivate proteins, especially enzymes.

Detail: most commonly seen with serine, threonine, and tyorsine

Question 21

Generally speaking, how does carboxylation affect proteins?

Answer 21

Addition of carboxylic acids. Carboxylating proteins is usually done so that the protein can have calcium binding sites.

Question 22

Generally speaking, how does glycosylation affect proteins?

Answer 22

Addition of oligosaccharides. Glycosylation is usually conducted in the ER and the golgi apparatus. Glycosylation is most often used as a signal for where the protein is supposed to end up in the cell. For example, a certain type of glycosylation might make a protein go to the lysosome while other glycosylations might make the protein go to the mitochondria.

Question 23

Generally speaking, how does prenylation affect proteins?

Answer 23

Prenylation (addition of lipid groups) is usually conducted on membrane bound enzymes so that they can associate with the membrane well.

Question 24

What is the main way that prokaryotes regulate how much of their genome they are expressing?

Answer 24

Operons

Question 25

What are the 5 main ways that Eukaryotes regulate how much of their genome they are expressing?

Answer 25

1. Transcription Factors 2. Enhancers 3. Gene duplication 4. Histone Acetylation 5. DNA methylation

Question 26

Describe the structure of an operon according to the Jacob-Monod model?

Answer 26

An operon is a cluster of genes transcribed as a single mRNA. The main pieces of an operon from left to right are the Regulator gene, the Promotor site, The Operator site, and The Structural gene Regulator gene- Codes for repressor Promoter site- Provides place for RNA pol to bind Operator site- Non transcribable region of DNA that can bind repressor Structural gene- codes for protein of interest

Question 27

What is an operon and what are the two types?

Answer 27

An inducible/ repressible cluster of genestranscribed as a single mRNA 1. Inducible Systems 2. Repressible Systems

Question 28

Describe an Inducible System operon?

Answer 28

In an inducible system, an ever-present repressor protein (coded for by the regulator) binds to the operator and stops RNA polymerase from transcribing it. However, if an inducer is present, then it will bind to the repressor and stop it from repressing the gene. This allows the operon to be transcribed. This is useful because it ties transcription of these genes to the presence of a specific molecule, which means that the gene is only on when the cell feels like it is needed. The classic inducible system is the lac operon, an operon that allows bacteria to digest lactose when it is in high enough concentrations. (they prefer glucose and thus don't need to produce lactase regularly) Negative inducible system

Question 29

What is a negative control mechanism?

Answer 29

Negative control mechanisms are systems in which the binding of a molecule reduces transcriptional activity. E.g. Repressor proteins

Question 30

What is a positive control mechanism?

Answer 30

A positive control mechanism is a system in which the binding of a molecule increases transcriptional activity. Example: CAP

Question 31

What is an inducer?

Answer 31

An inducer is a molecule that binds to a repressor to remove it from the operon.

Question 32

Describe a Repressible System operon

Answer 32

In a repressible system, an ever-present repressor protein (coded for by the regulator) cannot bind to the operator on its own, so RNA polymerase can transcribe it. However, if a co-repressor is present, then it will bind the repressor and allow it to repress the gene. This stops the operon from being transcribed. (Often negative feedback mechanisms, meaning product is co-repressor) This is useful because it ties transcription of these genes to the presence of a specific molecule, which means that the gene gets turned off when the cell feels its no longer needed. The classic repressible system is the trp operon, an operon that allows bacteria to synthesize trp when it is low in the cell. Negative repressible system

Question 33

What is an enhancer?

Answer 33

An enhancer is a group of reponse elements that bind elements (signal molecules bind to receptors which then act as transcription factors that bind to response element on DNA) far away from the gene in question in order to enhance the transcription of said gene. The large distance between the enhancer and the genes it enhances almost always lead to the DNA bending to bring them close together. Can be located within an intron. One enhancer for one gene (we don't have one enhancer helping multiple different promoters)

Question 34

What is Gene Duplication?

Answer 34

Gene duplication is when certain cells modify their genome by adding more copies of a gene (can be duplicated in sseries on the same chromosome and also in parallel by letting DNA pol replicate only that gene many times) As is expected, the more copies you have of a gene, the more you express the protein associated with the protein. For example, a skin cell might have many many copies of the keratin expressing gene because of its primary importance there.

Question 35

How exactly do histones get DNA to wrap so tightly?

Answer 35

Histones are studded with positively charged lysine residues, which bind tightly to the negative phosphate backbone of DNA.

Question 36

What is Histone Acetylation?

Answer 36

Histone acetylation is when the positively charged lysine residues are acetylated, which reduces their positive charge and weakens the binding of the histone with DNA. This results in loose DNA that can be more easily transcribed.

Question 37

What is DNA methylation?

Answer 37

DNA Methylation is when C and A Nucleotides are methylated. Methyl groups carry electron density in their bonds, which increases the negative charge of the DNA, which strengthens the interaction between histones and DNA. This results in tight DNA that is harder/unable to transcribe.

Question 38

What are chaperones?

Answer 38

Chaperones are a special protein that wraps around newly synthesized proteins in order to protect them and change the microenvironment in which the protein folds.

Question 39

What are the main three differences between DNA and RNA?

Answer 39

1. RNA has Ribose, DNA has Deoxyribose 2. RNA has Uracil, DNA has Thymine 3. RNA is single stranded, DNA is double stranded. (except in viruses!)

Question 40

What is the main difference between enhancers and promoters?

Answer 40

Enhancers are more than 25 base pairs away from the transcription site. Promoters are within 25 base pairs of the transcription site.